Samuel Hart, University of Washington Molecular and Cellular Biology PhD program
- Contact for questions regarding data analysis: sfhart33@gmail.com
Michael Metzger, Pacific Northwest Research Institute
- Contact for questions regarding Mya arenaria genome assembly: metzgerm@pnri.org
If you use any of these methods or data for your own research, please use the following citation:
- Hart S. F. M., Yonemitsu, M. A., Giersch, R. M., Garrett F. E. S., Beal B. F., Arriagada G., Davis B. W., Ostrander E. A., Goff S. P., Metzger M. J. (2023). Centuries of genome instability and evolution in soft-shell clam, Mya arenaria, bivalve transmissible neoplasia. Nature Cancer, doi:10.1038/s43018-023-00643-7.
- bedtools (2.29.1)
- BBTools (38.86)
- trimmomatic (0.36)
- bwa (0.7.12)
- samtools (1.9)
- somatypus (1.3)
- helmsman (1.5.2)
- bcftools (1.10.2)
- delly (0.8.5)
- seqtk (1.0)
- blast+ (2.10.0)
- CD-HIT (4.8.1)
- RepeatModeler (2.0)
- Repeatmasker (4.1.0)
- REPdenovo (2019.07.20 download)
- supernova (2.1.1)
- FALCON-Unzip (with pbbioconda-0.0.5 and python 3.7)
- FALCON-Phase (v0.1.0-beta)
- SNAP(version 2006-07-28)
- PBSuite (15.8.24, slightly modified: https://github.com/esrice/PBJelly)
- blasr (5.1)
- networkx (2.2 with Python 2.7)
- Longranger62 (2.2.2)
- FreeBayes (1.3.1)
- Trinity (2.8.5)
- MAKER (2.31.10)
- exonerate (2.2.0)
- BUSCO (v3)
- telseq (v0.0.2)
- STAR (2.7.5a_2020-06-29)
- Biostrings (2.54.0)
- sigfit (2.0.0)
- mapdata (2.3.0)
- maptools (1.1-1)
- tidyverse (1.3.0)
- ape (5.5)
- lsa (0.73.2)
- gridExtra (2.3)
- zoo (1.8-8)
- geiger (2.0.7)
- nlme (3.1-139)
- phytools (0.7-90)
- dndscv (0.0.1.0)
- devtools (2.3.2)
- cn.mops (1.32.0)
- mixtools (1.2.0)
- bedr (1.0.7)
- ggseqlogo (0.1)
- DESeq2 (1.26.0)
- pheatmap (1.0.12)
- RColorBrewer (1.1.3)
- viridis (0.5.1)
- scales (1.2.1)
Note that paths were designed for our institutes working environment: paths will need to be altered manually to reproduce this analysis